Lecture 4 Biological enrichment calculations and GO/GSEA

• splicing
• enrichment of SNPs in epigenomics data
• allele specific expression (ASE)

Any problem involving count data where the underlying probability is not known but a suitable “background” condition is available for comparison

• GOrilla
• Gene Set Enrichment Analysis (GSEA)

shamelessly stolen from: Hector Corrada Bravo

“In computer science and information science, an ontology encompasses a representation, formal naming and definition of the categories, properties and relations between the concepts, data and entities that substantiate one, many or all domains of discourse. More simply, an ontology is a way of showing the properties of a subject area and how they are related, by defining a set of concepts and categories that represent the subject.”

(from Wikipedia)

GeneOntology.org

• Molecular Function (e.g. “adenylate cyclase activity”)
• Cellular component (e.g. “ribosome”)
• Biological Process (e.g. “DNA repair”)

Reactome is an expert-authored, peer-reviewed knowledgebase of reactions and pathways.

• Manually curated human pathways with experimental evidence (regarded highest quality)
• Manually inferred pathways for other organism (e.g. Gallus gallus, Mus musculus)

Reactome is useful when…

• Know molecular details of a pathway based on literature (e.g. directed pathway)
• Learn crosstalk between pathways (e.g. shared genes/reactions)

Navigating Reactome

• Webpage provides an easy way to access, browse, analyse and download pathway data

Navigating Reactome

• Pathway browser

Navigating Reactome

• Pathway Structure

MSigDB

• Hallmark genesets
• Canonical pathways
• Regulatory Target genesets
• disease genesets
• many cancer sets
• Gene Ontology

• this is how genes relate to multiple terms

• this is how genes relate to multiple terms
• the usefulness of GO terms varies greatly throughout the graph